fix sanitizing of slashes and add sanitizing spaces

Delphine-L · Jun 28, 2024 · 6270c87 · 6270c87
1 parent fbaac02
commit 6270c87
Showing 1 changed file with 28 additions and 7 deletions.
diff --git a/tools/data_export/export_remote.xml b/tools/data_export/export_remote.xml
@@ -18,15 +18,35 @@ python '$__tool_directory__/export_remote.py'
         <configfile name="files_to_export">#import json
 #from galaxy.util import filesystem_safe_string
 #if $export_type.export_type_selector == "datasets_auto":
-#set $fileconfig = json.dumps($export_type.infiles.serialize(invalid_chars=tuple(str($invalid_chars))))
+	#if $invalid_chars=="space":
+		#set $fileconfig = json.dumps($export_type.infiles.serialize(invalid_chars=tuple(str(" "))))
+	#else:
+		#set $fileconfig = json.dumps($export_type.infiles.serialize(invalid_chars=tuple(str($invalid_chars))))
+	#end if
 #else if $export_type.export_type_selector == "collection_auto":
-#set $fileconfig = json.dumps($export_type.incollection.serialize(invalid_chars=tuple(str($invalid_chars)), include_collection_name=bool($export_type.include_collection_name)))
+	#set $fileconfig = json.dumps($export_type.incollection.serialize(invalid_chars=tuple(str($invalid_chars)), include_collection_name=bool($export_type.include_collection_name)))
+
+	#if $invalid_chars=="space":
+		#set $fileconfig = json.dumps($export_type.incollection.serialize(invalid_chars=tuple(str(" ")), include_collection_name=bool($export_type.include_collection_name)))
+	#else:
+		#set $fileconfig = json.dumps($export_type.incollection.serialize(invalid_chars=tuple(str($invalid_chars)), include_collection_name=bool($export_type.include_collection_name)))
+	#end if
+
 #else
-#set $fileconfig = [d['infile'].serialize() for d in $export_type.datasets]
-#for $i, $dataset in enumerate($export_type.datasets):
-    #silent $fileconfig[$i]['staging_path'] = filesystem_safe_string(str(dataset["name"]), 255, invalid_chars=())
-#end for
-#silent fileconfig = json.dumps($fileconfig)
+
+	#set $fileconfig = [d['infile'].serialize() for d in $export_type.datasets]
+	#if $invalid_chars=="space":
+		#for $i, $dataset in enumerate($export_type.datasets):
+			#silent $fileconfig[$i]['staging_path'] = filesystem_safe_string(str(dataset["name"]), 255, invalid_chars=[str(" ")])
+		#end for
+	#else:
+		#for $i, $dataset in enumerate($export_type.datasets):
+			#silent $fileconfig[$i]['staging_path'] = filesystem_safe_string(str(dataset["name"]), 255, invalid_chars=[str($invalid_chars)])
+		#end for
+	#end if
+
+	#silent fileconfig = json.dumps($fileconfig)
+
 #end if
 $fileconfig
         </configfile>
@@ -61,6 +81,7 @@ $fileconfig
         <param name="include_metadata_files" type="boolean" checked="true" label="Include metadata files in export?" help="Examples of metadata files are bam, cram and vcf indexes that can be regenerated from raw data" />
         <param name="invalid_chars" type="select" label="Select which characters should be stripped from the exported paths">
             <option value="/">Sanitize /</option>
+			<option value="space">Sanitize spaces</option>
             <option value="">Don't sanitize values</option>
         </param>
     </inputs>